Effect of cardiac resynchronization therapy on septal perfusion and septal thickening: Association with left ventricular function, reverse remodelling and dyssynchrony

BACKGROUND

We evaluated the effect of cardiac resynchronization therapy (CRT) on septal perfusion and thickening at 6 months post implantation assessed on Tc99m-MIBI Gated myocardial perfusion SPECT (GMPS).We also studied the association of change in septal perfusion and thickening with primary outcome defined as at least one [improvement in ≥1NYHA class, left ventricular ejection fraction (LVEF) by ≥ 5%, reduction of end-systolic volume (ESV) by ≥ 15%, and improvement ≥ 5 points in Minnesota living with heart failure questionnaire (MLHFQ)].

METHOD

One hundred and five patients underwent clinical and GMPS evaluation before and at 6 months post CRT.

RESULT

Post CRT there was significant improvement in mean normalized septal perfusion uptake and in septal thickening (P value = 0.001, both). There was no significant relation between improvement in septal perfusion and primary outcome. However, improvement in septal thickening was statistically significant with favorable primary outcome (P = 0.001).There was no significant correlation between improvement of septal perfusion and improvement in LVEF, reduction in End diastolic volume (EDV), ESV, and Left ventricular Dyssynchrony (LVD). But, there was significant correlation between improvement of septal thickening and these parameters.

CONCLUSION

Improvement in septal thickening was associated with reverse remodeling, improvement in LVEF, and reduction of LVD.

A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence

Glioma diagnosis is based on histomorphology and grading; however, such classification does not have predictive clinical outcome after glioblastomas have developed. To date, no bona fide biomarkers that significantly translate into a survival benefit to glioblastoma patients have been identified. We previously reported that the IDH mutant G-CIMP-high subtype would be a predecessor to the G-CIMP-low subtype. Here, we performed a comprehensive DNA methylation longitudinal analysis of diffuse gliomas from 77 patients (200 tumors) to enlighten the epigenome-based malignant transformation of initially lower-grade gliomas. Intra-subtype heterogeneity among G-CIMP-high primary tumors allowed us to identify predictive biomarkers for assessing the risk of malignant recurrence at early stages of disease. G-CIMP-low recurrence appeared in 9.5% of all gliomas, and these resembled IDH-wild-type primary glioblastoma. G-CIMP-low recurrence can be characterized by distinct epigenetic changes at candidate functional tissue enhancers with AP-1/SOX binding elements, mesenchymal stem cell-like epigenomic phenotype, and genomic instability. Molecular abnormalities of longitudinal G-CIMP offer possibilities to defy glioblastoma progression.

Shared dysregulation of long non-coding RNA and developmental gene networks in histone H3 K27M gliomas and PF-A ependymomas

e21523

Background: Diffuse pediatric gliomas harboring a Histone-H3 K27M mutation are more aggressive than H3-wild type gliomas and demonstrate global hypomethylation at the K27 residue1. As a result, these tumors show global aberrant gene expression, resulting in a stem-like proliferative cell population2. Posterior fossa (PF) ependymomas, on the other hand, harbor few significantly recurrent somatic mutations, but PF-A and PF-B subgroups have been defined on the basis of epigenetic differences3. Compared to PF-B, the PF-A subgroup demonstrates H3K27 hypomethylation, aberrant gene expression and aggressive tumor growth4,5. Methods: We recently identified a set of long non-coding RNA (lncRNA) that are transiently expressed in early brain development6, and hypothesized that H3K27M gliomas and PF-A ependymomas may share methylation-related dysregulation of lncRNA networks responsible for maintaining normal differentiation programs. Results: Here we describe a network of regulatory lncRNA with increased expression in both H3K27M gliomas and PF-A ependymomas, as compared to H3-WT gliomas and PF-B ependymomas. We demonstrate that increased expression of this lncRNA network correlates with the over-expression of signaling pathways involved in maintaining a non-differentiated, proliferative phenotype and driving tumorigenesis. Conclusions: We hypothesize that in both H3K27M gliomas and PF-A ependymomas, aberrant global methylation may be driving lncRNA to activate and maintain stem-like states in early neural development, suggesting similarities in epigenetically driven, developmental origins for both tumor types. References: 1. Chan KM, Fang D, Gan H, et al. Genes Dev. 2013;27(9):985-90; 2. Filbin MG, Tirosh I, Hovestadt V, et al. Science. 2018;360(6386):331-5; 3. Witt H, Mack SC, Ryzhova M, et al. Cancer cell. 2011;20(2):143-57; 4. Bayliss J, Mukherjee P, Lu C, et al. Sci. Transl. Med. 2016;8(366):366ra161; 5. Mack SC, Witt H, Piro RM, et al. Nature. 2014;506(7489):445; 6. Field AR, Jacobs FM, Fiddes IT, et al. bioRxiv. 2017:232553.

Abstract A22: Identification of gene expression differences between primary pediatric tumors and their PDX models

Molecularly targeted therapies inhibit specific cancer pathways and have fewer harmful side effects than cytotoxic chemotherapies; however, the development of targeted therapies for childhood cancers has lagged behind that of adult cancers. Although adult and childhood cancers have different molecular mechanisms, similar druggable cancer pathways may be activated. We propose using gene expression analysis to identify opportunities to reposition FDA-approved targeted therapies for childhood cancer patients. We developed an N-of-1 gene expression approach that leverages a compendium of ~11,000 cancer gene expression profiles. To evaluate the utility of this approach for identifying cancer driver pathways, we analyzed gene expression data for 9 patient-derived xenograft (PDX) tumors. PDXs were tested for sensitivity to selected targeted therapies. Our analysis correctly predicted drug sensitivity in 8 of the 9 PDXs based on overexpression of specific cancer pathways. We also compared gene expression between PDX and matched primary tumor samples (n=7). Using TumorMap analysis, we found that PDX tumors cluster with their matched primary tumor and other samples with a similar cancer diagnosis. We also ran differential expression analysis and found 260 overexpressed genes and 630 underexpressed genes in PDX tumors. Underexpressed genes were associated with immune functions, extracellular matrix proteins, and growth factor signaling. Overexpressed genes were involved in TNF-α; signaling. This analysis confirmed expected changes in gene expression while also identifying TNF-α; signaling as a potential biologic artifact of PDX tumors. These features may influence the results of PDX experiments and should be accounted for when using this model. Overall, the PDX model recapitulates gene expression features of pediatric cancer and is a powerful tool for evaluating novel precision medicine approaches.

Citation Format: Jacob J. Pfeil, Alex G. Lee, Leanne C. Sayles, Ellen T. Kephart, Holly C. Beale, Lauren M. Sanders, Olena Morozova, Sofie R. Salama, Alejandro Sweet-Cordero, David Haussler. Identification of gene expression differences between primary pediatric tumors and their PDX models [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A22.

FEATURES OF HEMODYNAMICS IN VERTEBROBASILAR ARTERIAL SYSTEM IN YOUNG PEOPLE, DEPENDING ON BIOMECHANICAL DISORDERS OF THE MUSCULOSKELETAL SYSTEM

In order to study the features of hemodynamics in the vertebral artery (VA), depending on the biomechanical disorders of the cervical spine (CS) and the musculoskeletal system as a whole 105 patients (53 females and 52 males, mean age - 38±5,9 years) having signs of the Vertebrobasilar insufficiency on the background of biomechanical disorders of the CS and the locomotor system as a whole were examined. The control group included 50 practically healthy persons (25 females and 25 males, mean age - 37±5,6 years). Physical examination included a clinical-neurological, vertebro-neurological examination (visual assessment of violations of statics and dynamics of the musculoskeletal system, measuring the craniovertebral angle (CVA) using a photogrammetric method, manual diagnostics for the detection of muscular-tonic syndromes and musculoskeletal dysfunction) and Doppler ultrasound of extra- and intracranial segments of VA. It was revealed the relationship between the violation of hemodynamics in vertebrobasilar system and pathobiomechanical changes of the musculoskeletal system in patients of young age. The leading pathogenetic role in the onset of hemodynamic disorders in VA belongs to a non-optimal static stereotype in the cervical region in the form of displacement of the regional center of gravity forward with the formation of a forward head position. It was revealed a positive correlation between the value of CVA and the degree of mobility of the craniovertebral transition by A. Stoddart (r = +0.79, p <0.05) and also - a negative correlation between CVA value and the level of blood flow reduction in VA during functional rotational tests (r=-0,69, p<0,05).

Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer

Clinical detection of sequence and structural variants in known cancer genes points to viable treatment options for a minority of children with cancer.¹ To increase the number of children who benefit from genomic profiling, gene expression information must be considered alongside mutations.^2,3 Although high expression has been used to nominate drug targets for pediatric cancers,^4,5 its utility has not been evaluated in a systematic way.⁶ We describe a child with a rare sarcoma that was profiled with whole-genome and RNA sequencing (RNA-Seq) techniques. Although the tumor did not harbor DNA mutations targetable by available therapies, incorporation of gene expression information derived from RNA-Seq analysis led to a therapy that produced a significant clinical response. We use this case to describe a framework for inclusion of gene expression into the clinical genomic evaluation of pediatric tumors.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111-4. ©2017 AACR.

Abstract LB-338: A critical evaluation of genomic data sharing: Barriers to accessing pediatric cancer genomic datasets: a Treehouse Childhood Cancer Initiative experience

Genomic data sharing is increasingly recognized as critical to genomic research. The need is acute in pediatric cancer research due to the rarity of pediatric tumor types and paucity of pediatric cancer data, and in translational research to assess the impact of genomic research on human health. However, genomic data sharing is hindered by an absence of standards regarding timing, patient privacy, use agreement standards, and data characterization and quality. At UC Santa Cruz Treehouse Childhood Cancer Initiative (treehousegenomics.soe.ucsc.edu), we examine individual pediatric cancer tumor RNA sequencing profiles against a database of over 11,000 tumor RNA sequencing profiles from public genomic datasets such as The Cancer Genome Atlas, Therapeutically Applicable Research To Generate Effective Treatments, International Cancer Genome Consortium, and Medulloblastoma Advanced Genomics International, and pediatric cancer clinical trials with which we partner, such as those at Stanford University, UC San Francisco, Children’s Hospital of Orange County, and British Columbia Children’s Hospital. For over 18 months, we have worked systematically to enhance the Treehouse dataset by adding pediatric cancer data and presently underrepresented tumor types. The NIH and other leading funding agencies now regularly require grantees to make genomic data generated available to the research community, either post-publication or after an embargo period. We have combed websites and public repositories, searched PubMed, and contacted researchers directly. Finding data requires a mining of literature, often with limited information, and initiating the many different processes for requesting permission for these datasets, with different and often cumbersome data use obligations. The combination of cryptically named datasets, multiple data types and the practice of grouping datasets from multiple papers under a single study accession makes zeroing in on the correct dataset challenging. Downloading the genomic data is time-consuming, such that a dataset of under a 100 files can take up to a week to download under optimal conditions. Matching metadata is inconsistently available, often vague, sparse or error ridden. Only after months of identifying, permissioning for use, committing to use- and sharing-restricting terms, and downloading the genomic and metadata, is it possible to assess the quality, often discovering that data quality is low. We evaluate the barriers to data sharing based on the Treehouse experience and offer guidelines for timing, use agreement standards, and data characterization and quality, to enhance data sharing and outcomes for all pediatric cancer patients.

Citation Format: Katrina Learned, Ann Durbin, Robert Currie, Holly Beale, Du Linh Lam, Theodore Goldstein, Sofie R. Salama, David Haussler, Olena Morozova, Isabel Bjork. A critical evaluation of genomic data sharing: Barriers to accessing pediatric cancer genomic datasets: a Treehouse Childhood Cancer Initiative experience [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-338. doi:10.1158/1538-7445.AM2017-LB-338

Abstract 2466: Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing

In the UC Santa Cruz Treehouse Childhood Cancer Initiative (treehousegenomics.soe.ucsc.edu), we are exploring the utility of using RNA-Seq analysis of tumor samples from children to identify potential novel therapeutic options for each individual. Within a single RNA-Seq data set, the gene expression measurements are not equally accurate. The identification of activated, druggable pathways requires accurate gene-level expression measurements.

We receive samples from a variety of clinical and research settings, and the quantity and complexity of the available input material and the depth of sequencing differ. These factors inspired us to develop a tool that will allow us to identify accurate measurements in most RNA-Seq samples we receive.

First, we characterized the relationship between depth of sequencing and the accuracy of the gene expression measurement. We analyzed subsets of reads in samples with more than 50 million Uniquely Mapped, Exonic, Non-duplicate (UMEND) reads. UMEND reads typically constitute over 80% of the reads in a high quality experiment with sufficient starting material. We compared gene expression across the subsets of reads to calculate how many UMEND reads are required to produce consistent measurements. We found that, on average, genes expressed at 1-5 TPM in our data require 30 million reads to be accurately measured. For this calculation, we define accuracy as the condition in which 75% of genes are measured to within 25% of the true value.

Secondly, we use these known relationships to identify genes that have been accurately measured in our tumor RNA-Seq samples. For a sample with 15 million UMEND reads, we find that genes expressed above 5 TPM can be accurately measured and are retained. In the first twelve samples analyzed, samples with more than 10 million UMEND reads retained at least 46% of the genes expressed above zero. We exclude as references those samples with fewer than 10 million UMEND reads due to the marked gene loss after thresholding for this group.

Using accurately measured genes allows us to more confidently assess similarity to other samples, identify enriched pathways, and confirm the expression of drug targets and related molecules under consideration. For example, we reconsidered the CDK4 inhibitor Palbociclib in one patient because the expression of RB1, downstream effector required for Palbociclib-mediated tumor cell death, was under our accuracy threshold. Accuracy thresholds can also be used in experiment planning.

Accuracy thresholding allows us to better assess the value of an RNA-Seq data set and, if necessary, identify the subset of genes whose expression can be confidently considered in a clinical setting. Our experience points to the importance of careful quality control in this process.

Citation Format: Holly Beale, Du Linh Lam, John Vivian, Yulia Newton, Avanthi Tayi Shah, Isabel Bjork, Ted Goldstein, Angela N. Brooks, Josh Stuart, Sofie Salama, E. Alejandro Sweet-Cordero, David Haussler1, Olena Morozova. Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2466. doi:10.1158/1538-7445.AM2017-2466

Abstract 4890: A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data

Genomic characterization used in pediatric cancer clinical trials is limited to the detection of somatic mutations and gene fusions in well-characterized cancer genes. However, these approaches do not reveal actionable therapeutic targets for the majority of pediatric cancer patients. Incorporation of gene expression information into clinical genomic analysis is hindered by the lack of appropriate computational methods, designed for single patients rather than patient cohorts. UC Santa Cruz Treehouse Childhood Cancer Initiative (treehousegenomics.soe.ucsc.edu) enables the incorporation of gene expression information into the genomic evaluation of pediatric cancer patients. We leverage large cancer RNA sequencing datasets, including The Cancer Genome Atlas, Therapeutically Applicable Research to Generate Effective Treatments, Medulloblastoma Advanced Genomics International Consortium, International Cancer Genome Consortium, and published research and clinical studies. Through our “pan-cancer analysis”, we compare each prospective tumor’s RNA sequencing and/or mutational profile to over 11,000 uniformly analyzed tumor profiles using our Tumor Map method. Tumor Map visualizes single tumors together with the reference compendium and identifies samples that are most similar to the given tumor based on the gene expression profiles. We also developed a gene expression outlier analysis to identify transcripts that are over expressed in the given tumor. These pan-cancer gene expression analyses are used in conjunction with mutation data to nominate molecular pathways that may be driving the disease in each child, providing useful information to the medical teams. We aim to evaluate this approach in partnership with pediatric cancer clinical genomic trials at Stanford University, UC San Francisco, Children’s Hospital of Orange County, University of Michigan, Children’s Mercy Hospital, and British Columbia Children’s Hospital. The analysis of the first 27 patients at Stanford, most with refractory solid tumors, provided evidence of the potential clinical utility of incorporating gene expression information into the genomic evaluation of pediatric cancer patients. In all cases, we identified candidate driver molecular pathways that could be targeted by existing FDA-approved therapies or therapies available through a clinical trial. The most frequently identified molecular targets were receptor tyrosine kinases and cyclin-dependent kinases. For 3 patients with no treatment options prior to our work, the analysis contributed to treatment decisions. This study provides a framework for incorporating gene expression information into the clinical interpretation of pediatric cancer genomic data. We underscore the importance of releasing the data to the community immediately following generation, so that they may benefit new patients.

Citation Format: Olena Morozova, Yulia Newton, Avanthi Tayi Shah, Holly Beale, Du Linh Lam, John Vivian, Isabel Bjork, Theodore Goldstein, Josh Stuart, Sofie Salama, E. Alejandro Sweet-Cordero, David Haussler. A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4890. doi:10.1158/1538-7445.AM2017-4890

Comparative genomic analysis for pediatric cancer patients evaluated in a California Initiative to Advance Precision Medicine Demonstration Project

TPS10578

Background: California Kids Cancer Comparison (CKCC), a demonstration project for the California Initiative to Advance Precision Medicine, evaluates the utility of incorporating gene expression information into the genomic analysis of difficult-to-treat pediatric cancers. CKCC is a partnership between UC Santa Cruz and clinical genomic trials conducted by Children’s Hospital of Orange County, UC San Francisco (Pacific Pediatric Neuro Oncology Consortium), and Stanford University. Methods: CKCC compares each prospective tumor’s RNA sequencing profile to over 11,000 uniformly analyzed tumor profiles from pediatric and adult cancer patients. These comparisons are used to identify genes and pathways that are significantly over expressed in each patient’s tumor. The pathways are reviewed by data analysis for the potential for clinical impact and presented to the treating oncologist in a molecular tumor board setting.

Abstract LB-290: UCSC TumorMap: Exploring cancer signatures on an interactive dynamic landscape

Cancer is caused by accumulated changes in a cell's DNA sequence that disrupt the regulation of genetic networks. Mutation type, cell of origin, and tissue microenvironment all influence the initiation and progression of disease. The Cancer Genome Atlas (TCGA) catalogues the molecular changes of thousands of tumor samples of various tumor types using different data modalities including genomic, transcriptomic, proteomic, and epigenomic views. The goal is to find similarities amongst cancers of different tissues and to reveal clinically-relevant subtypes sharing common molecular abnormalities. While various analyses for interpreting these rich datasets exist, few methods are available to enable intuitive global overviews of these rich compendia. There is a need for methods that can tap the statistical power of large cohorts, to aid in analysis of smaller cohorts and of individual patient samples. Patterns present in many tumors may reveal driving genomic aberrations and pathway signatures that inform therapy. Here, we present a TumorMap, a tool that generates a map of cancer samples for interactive exploration, data overlay visualization, and statistical analysis. TumorMap arranges samples on a hexagonal 2-dimensional grid based on sample similarity. Different maps can be made for each distinct platform of data. Herein we demonstrate the utility of TumorMap for revealing commonalities between cancers of different tissue types, and its ability to aid in pan-cancer hypothesis generation. TumorMap maps for various cancer cohorts are available for free online at http://tumormap.ucsc.edu.

Citation Format: Yulia Newton, Adam Novak, Teresa Swatlowski, Sahil Chopra, Sofie Salama, Olena Morozova, David Haussler, Joshua Stuart. UCSC TumorMap: Exploring cancer signatures on an interactive dynamic landscape. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-290.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.

Abstract PR14: Harnessing the power of big data to advance pediatric cancer care

DNA and RNA sequencing is increasingly applied in clinical trials to find new therapeutic leads for children with incurable cancers. However, compared to similar studies in adults, these trials have yielded fewer new treatment options, because pediatric and adult malignancies are distinct biologically, and far less data are available on the genomics of pediatric tumors. Initiatives such as the National Cancer Institute's (NCI) Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project, and the Medulloblastoma Advanced Genomics International Consortium (MAGIC) have generated large cohorts through collaboration, however they are limited to specific diseases. In addition, there is no mechanism to integrate these data with genomic data collected in prospective precision medicine trials. The failure to share data has meant that available genomic information is not being utilized to its full potential, resulting in missed therapeutic opportunities.

The UC Santa Cruz Treehouse Childhood Cancer Project integrates genomic data generated by pediatric research studies, such as TARGET, MAGIC, the Pediatric Cancer Genome Project, and the Childhood Brain Tumor Tissue Consortium with genomic data generated by clinical trials. Treehouse also makes it possible to compare these data with large adult datasets, including The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC), and Stand Up to Cancer (SU2C). Together, these datasets provide access to the genomic information from over 15,000 individual tumors that can be used as context for real-time data interpretation from individual patients in clinical genomics trials. This work presents a case report that illustrates how integrating multiple pediatric and adult gene expression datasets with similar data collected from patients in a prospective clinical trial can provide new clinical leads for children with difficult-to-treat cancers. The data are integrated and analyzed using TumorMap, an unsupervised clustering and visualization approach that has been shown to reveal new clinical insights into adult cancers as part of the TCGA Pan-Cancer effort. The expression of individual genes and their relationship with phenotypic features in the combined cohort can be visualized using the UCSC Xena Bowser. New clinical leads can be recommended for individual patients based on the similarity of their molecular profiles to those of other cancers with available treatment options, as shown in the TumorMap. We propose to extend our case study to a framework of how genomic datasets collected from adult and pediatric patients in research and clinical settings can be used to inform the care of pediatric patients prospectively. This framework will provide new hope for children with difficult to treat cancers so that no therapeutic option is overlooked in the fight to save their lives.

Citation Format: Olena Morozova, Yulia Newton, Melissa Cline, Stephen Yip, Arjun Rao, Josh Stuart, Ted Goldstein, Sofie Salama, Rebecca Deyell, S. Rod Rassekh, David Haussler. Harnessing the power of big data to advance pediatric cancer care. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr PR14.

Abstract A2-52: Pan-cancer analysis reveals distinct effects of receptor tyrosine kinase mutations on downstream pathway activities

Receptor tyrosine kinases (RTKs) are a diverse group of trans-membrane proteins that control cellular growth, survival and differentiation. Constitutive activation of RTKs is a hallmark of cancers, and can occur via copy number amplifications, point mutations, gene fusions or combinations of these events. Several RTKs are important anti-cancer targets that can be inhibited by small molecules and antibodies. Treatments with RTK inhibitors have had promising results in some cancers with RTK alterations (e.g., non-small cell lung cancer), but limited effectiveness in others (e.g., glioblastoma multiforme). This discrepancy warrants further study of the RTK pathway alterations in glioblastoma and across different cancer types.

Seventy-nine percent of TCGA glioblastoma multiforme (GBM) tumors with wild type IDH1 and IDH2 (IDHwt) harbor at least one somatic alteration in genes associated with the RTK signaling pathway. These include aberrations in RTKs themselves (EGFR, FGFR, MET, NTRK and PDGFR) or downstream components of their signaling (PI3K complex and PTEN). Of these, alterations in EGFR are most frequent and occur in over 45% of IDHwt GBM cases, including EGFR amplifications (32%), point mutations (4%), and combinations of amplifications and point mutations (15%). Our analysis of the TCGA lower-grade glioma (LGG) cohort revealed similar patterns of RTK signaling activation in 73% of IDHwt LGGs. In the IDHwt LGG cohort, EGFR amplifications occur in 11% of cases, point mutations in another 10% of cases, and multiple EGFR alterations in an additional 16% of cases.

Along with amplifications and point mutations, fusions of FGFR, EGFR and NTRK have been reported in IDHwt GBM and found to occur in IDHwt LGGs by our group. Based on this work, targeting RTKs other than EGFR has emerged as a potential treatment strategy for IDHwt gliomas. While activating RTK events in gliomas and other cancers are well known, their effect on downstream pathway signaling has not been fully elucidated. First, it is unclear whether the different mechanisms of RTK activation have similar effects on downstream pathway activity. Second, it is unknown how multiple types of RTK activation that occur in the same patient interact together to impact the signaling cascade. To address these questions, we used PARADIGM pathway analysis to estimate RTK pathway activity across 28 TCGA tumor types, including LGG and GBM. We then used PARADIGM-Shift to explore the effects of different types of RTK pathway alterations on the downstream signaling cascade. Our analysis implicates FGFR, NTRK and EGFR fusions as the strongest activators of RTK signaling in IDHwt gliomas. We also show that multiple RTK alterations in the same sample produce stronger pathway activation than single alterations. These experiments provide a framework for predicting sensitivity to RTK inhibitors across cancer types.

Citation Format: Olena Morozova, Sam Ng, Arjun Rao, Josh Stuart, David Haussler, Sofie Salama. Pan-cancer analysis reveals distinct effects of receptor tyrosine kinase mutations on downstream pathway activities. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-52.

Abstract 2976: Comprehensive Pan-Genomic characterization of adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare neoplasm with a heterogeneous outcome and limited treatment options. To understand its molecular and genomic landscape as a part of The Cancer Genome Atlas (TCGA) project, we performed the genomic, transcriptomic, epigenomic and proteomic profiling of 91 ACCs.

We identified potential driving alterations including amplifications (TERT, TERF2 and CDK4), deletions (ZNRF3, CDKN2A and RB1) and point mutations in genes unknown to participate in adrenal disease (RPL22) and genes known to initiate familial syndromes that occasionally include adrenocortical neoplasms (TP53, CTNNB1, PRKAR1A, MEN1). The finding of PRKAR1A expands the catalogue of pathogenic pathways underlying ACC, suggesting of the protein kinase alpha signaling pathway as a potential target for molecular interventions. Novel transcript fusions potentially leading to overactive kinases included EXOSC10-MTOR and PPP1CB-BRE.

DNA copy number analysis unveiled prevalent DNA losses leading to hypodiploidy as well as whole genome doubling (WGD) in 51% of ACC. The similar penetrance of loss of heterozygosity before and after WGD suggests a sequential development from hypodiploidy to polyploidy along the doubling in a subset of ACCs, which was endorsed by the worse outcome for WGD samples relative to nonWGD ACCs. An association between TERT expression and WGD was observed, suggesting a role for telomere regulation. These findings present ACC as a model disease for studies of WGD which is a frequent event in many tumor types.

Unsupervised clustering of DNA methylation, copy number, gene expression, miRNA expression and protein abundance converged into three classes with specific biological characteristics and a respective median event free survival of 8, 38 and &gt;100 months (p-value 1.7e-13). Comparison of the subtypes suggested additional drivers such as protein kinase C (PKC) phosphorylation and upregulation of a miRNA cluster at chromosome Xq27.3, which complemented the genomic alterations identified in these subtypes.

To gain more insights into this rare cancer type, we placed ACC in a broader context of cancer genomic profiles including an array of other cancer types. These analyses revealed interesting shared features, including beta-catenin activation with a subset of endometroid cancer, DNA mismatch repair gene mutational signature with gastrointestinal cancers and a smoking signature with lung cancer. These findings highlight the commonalities between ACC and other lineages of cancer.

Taken together, we found Wnt signaling pathway and p53/Rb signaling pathway were the most frequently altered pathways in ACC. Meanwhile, new players surfaced from our analyses including the PKA and PKC pathways. Our results present a comprehensive genomic landscape and refined molecular classification of ACC improve our understanding of its pathogenesis, and will ultimately improve the care of patients.

Citation Format: Siyuan Zheng, Andrew D. Cherniack, Ninad Dewal, Richard A. Moffitt, Ludmila Danilova, Bradley A. Murray, Antonio M. Lerario, Tobias Else, Theo A. Knijnenburg, Giovanni Ciriello, Seungchan Kim, Guillaume Assie, Olena Morozova, Rehan Akbani, Juliann Shih, Katherine A. Hoadley, Toni K. Choueiri, Jens Waldmann, Ozgur Mete, Gordon A. Robertson, Matthew Meyerson, Michael J. Demeure, Felix Beuschlein, Anthony Gill, Ana C. Latronico, Maria C. Fragosa, Leslie Cope, Electron Kebebew, Mouhammed A. Habra, Timothy G. Whitsett, Kimberly J. Bussey, William E. Rainey, Sylvia Asa, Jérôme Bertherat, Martin Fassnacht, David A. Wheeler, The Cancer Genome Atlas Research Network, Gary D. Hammer, Thomas J. Giordano, Roel Verhaak. Comprehensive Pan-Genomic characterization of adrenocortical carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2976. doi:10.1158/1538-7445.AM2015-2976

Abstract LB-212: Treehouse Childhood Cancer Project: a resource for sharing and multiple cohort analysis of pediatric cancer genomics data

Deep sequencing of adult and pediatric tumors revealed that different cancers share common genetic mutations. Aside from sequence mutation, gene expression, copy number, and epigenetic mechanisms contribute to tumorigenesis, and integrating this information may reveal more aberrant signaling pathways than analysis of mutations alone. Significantly, agents targeting specific pathways may be effective against multiple malignancies, regardless of the mechanisms of pathway deregulation. These observations suggest that pediatric cancer patients may benefit from targeted therapies developed for adults. Since the development of pediatric-cancer-specific therapies is hindered by the limited involvement of pharmaceutical companies and small patient cohorts, repositioning drugs designed for adult tumors remains the fastest and most effective way to bring new treatment options to pediatric cancer patients

While pediatric tumors have been characterized by genome-wide technologies, the data from these studies are typically under-utilized beyond the initial single cohort, single data type analyses. Consequently, we still lack a comprehensive picture of the molecular pathways that contribute to pediatric cancer in each patient, especially those that can be targeted in the clinic. Integrating multiple datasets is essential for assembling large enough patient cohorts to achieve an understanding of cancer-driving molecular aberrations in individual patients.

The Treehouse Childhood Cancer Project consolidates gene expression, mutation and copy number datasets under the UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu), and currently contains data from over 1000 pediatric tumors from TARGET and other studies. Treehouse enables mining these data alongside the data from adult cancers studied by The Cancer Genome Atlas consortium (TCGA). This is accomplished using bioinformatics tools developed for the TCGA Pan-Cancer Analysis Working Group and aimed at identifying situations where a subset of pediatric tumors may be driven by similar molecular pathways as adult tumors. We have assembled a consortium of researchers who plan to both contribute data to the Treehouse platform and apply Treehouse data in their analyses. These include John Maris (Children's Hospital of Philadelphia), Michael Taylor (Hospital for Sick Children, Toronto), Poul Sorensen (University of British Columbia), Timothy Triche (Children's Hospital Los Angeles), Soheil Meshinchi (Fred Hutchinson Cancer Research Center), Doug Hawkins (Seattle Children's Hospital), Javed Khan (NIH Center for Cancer Research), Ching Lao (Texas Children's Hospital), Leonard Sender (UC Irvine, Children's Hospital of Orange County), Alejandro Sweet-Cordero (Stanford School of Medicine), and D.W. Parsons (Baylor College of Medicine).

In this submission, we demonstrate the utility of the Treehouse resource by analyzing the neuroblastoma TARGET cohort in the context of adult TCGA cancers. This work presents a proof of concept that cross-cancer multiple cohort analysis can lead to new insights into pediatric malignancies.

Citation Format: Olena Morozova, Yulia Newton, Melissa Cline, Jingchun Zhu, Katrina Learned, Josh Stuart, Sofie Salama, Robert Arceci, David Haussler. Treehouse Childhood Cancer Project: a resource for sharing and multiple cohort analysis of pediatric cancer genomics data. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-212. doi:10.1158/1538-7445.AM2015-LB-212

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

BACKGROUND

Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas.

METHODS

We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes.

RESULTS

Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma.

CONCLUSIONS

The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.).

The UCSC Cancer Genomics Browser: update 2015

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations. Users can explore the relationship between genomic alterations and phenotypes by visualizing various -omic data alongside clinical and phenotypic features, such as age, subtype classifications and genomic biomarkers. The Cancer Genomics Browser currently hosts 575 public datasets from genome-wide analyses of over 227 000 samples, including datasets from TCGA, CCLE, Connectivity Map and TARGET. Users can download and upload clinical data, generate Kaplan–Meier plots dynamically, export data directly to Galaxy for analysis, plus generate URL bookmarks of specific views of the data to share with others.

Abstract A33: Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) is a set of web-based tools to display, investigate and analyze cancer genomics data and associated clinical data. Experimental quantities such as gene expression levels, copy number variation and somatic mutations are displayed next to clinical features such as age of onset and cancer subtype. Users can interactively group or sort data by clinical features to dynamically explore how genomic aberrations relate to clinical outcomes. Integrated Kaplan–Meier plots help investigators assess how clinical or genomic values impact long-term survival. The browser currently hosts data from 144 cancer studies including TCGA, CCLE and LINCS. It can display data from multiple studies at once, facilitating cross-cancer comparisons.

We are currently interested in hosting new pediatric cancer datasets, and can offer either public or protected access as appropriate.

Figure 1 illustrates the power of this approach. It compares patterns of somatic mutations in pediatric high-risk neuroblastoma, a cancer of the peripheral nervous system (Pugh, Morozova et al, Nature Genetics 2013) to those in two adult cancers of the central nervous system: lower grade glioma (LGG, TCGA) and glioblastoma multiforme (GBM, TCGA), and contrasts the age of the patient with frequency of mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-linked (ATRX) gene. The data for all three cancers is sorted by the age of the patient, with yellow being the oldest. The age ranges overlap: the oldest neuroblastoma patients are 16, while the youngest LGG and GBM patients are 14 and 21 respectively. While the three cancers show distinct patterns of somatic mutations, all three show frequent mutations in the ATRX gene in older teens or young adults.

This suggests that these cancers may share age-related subtypes with similar genomic signatures. These subtypes may indicate the age-dependent importance of ATRX in the development of both central and peripheral nervous systems, and may ultimately highlight common therapeutic avenues for the two groups of diseases.

This data set can be explored at the UCSC Cancer Genomics Browser at https://genome-cancer.ucsc.edu/proj/site/hgHeatmap/#?bookmark=pc

Citation Format: Melissa Cline, Olena Morozova, Teresa Swatloski, Brian Craft, Mary Goldman, David Haussler, Jingchun Zhu. Exploring pediatric cancer genomics with the UCSC Cancer Genomics Browser. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A33.

A phosphoproteomics approach to identify candidate kinase inhibitor pathway targets in lymphoma-like primary cell lines

Mass spectrometry-based technologies are increasingly utilized in drug discovery. Phosphoproteomics in particular has allowed for the efficient surveying of phosphotyrosine signaling pathways involved in various diseases states, most prominently in cancer. We describe a phosphotyrosine-based proteomics screening approach to identify signaling pathways and tyrosine kinase inhibitor targets in highly tumorigenic human lymphoma-like primary cells. We identified several receptor tyrosine kinase pathways and validated SRC family kinases (SFKs) as potential drug targets for targeted selection of small molecule inhibitors. BMS-354825 (dasatinib) and SKI-606 (bosutinib), second and third generation clinical SFK/ABL inhibitors, were found to be potent cytotoxic agents against tumorigenic cells with low toxicity to normal pediatric stem cells. Both SFK inhibitors reduced ERK1/2 and AKT phosphorylation and induced apoptosis. This study supports the adaptation of high-end mass spectrometry techniques for the efficient identification of candidate tyrosine kinases as novel therapeutic targets in primary cancer cell lines.

Abstract 3804: Rare DNA variants are enriched at the BARD1 locus and likely influence neuroblastoma susceptibility

BACKGROUND: A genome-wide association study (GWAS) in neuroblastoma identified 8 regions where common polymorphisms are associated with neuroblastoma susceptibility. However, the biological mechanisms and causal SNPs are largely unknown. Rare variants, potentially in linkage with common polymorphisms but with a higher effect size, may contribute to cancer susceptibility at GWAS-defined loci and provide biological insight into mechanism.

METHODS: To identify rare variants at neuroblastoma GWAS loci we performed ultradeep targeted resequencing of BARD1 and LMO1 on peripheral blood DNA using RainDance microdroplet RDT1000 PCR enrichment, and HiSeq2000 single end 100 bp reads. We aggregated existing whole-genome and exome sequence data from constitutional DNA of neuroblastoma cases (Molenaar et al, Nature 2012; NCI TARGET) on all replicated neuroblastoma GWAS regions.

RESULTS: Exon sequence data were available for 517 cases for BARD1, and 330 cases for LMO1, LINC00340, LIN28B-HACE1, LMO1, DUSP12, DDX4-IL3RA, and HSB17B12 (all genes with replicated associations to NB). The highest frequency of rare potentially damaging variants occurred in BARD1 with 7/517 cases (1.4%) containing novel (n=4) or rare (n=3) variants as defined by ESP6500, 1000 genomes project, and dbSNP135. Rare variants at BARD1 were associated with homozygosity or heterozygosity for the protective alleles. Using SIFT, PolyPhen-2 or MutationTaster, 6/7 variants were predicted to be deleterious, including a nonsense mutation in the domain mediating BARD1-BRCA1 heterodimerization and a nonsense mutation in a BRCT domain implicated in homology directed repair. Sanger sequencing of tumor DNA and RNA confirmed both nonsense mutations were present in their respective primary tumors. HEK293 cells transfected with BARD1 nonsense variants showed decreased stabilization of BRCA1.

CONCLUSION: Novel and potentially damaging mutations in BARD1 exons are present in the constitutional DNA of ∼1% of patients with neuroblastoma and may contribute to disease susceptibility. However, BARD1 rare variants were not tagged by the common risk alleles providing an alternative mechanism to prime neuroblasts towards transformation. Further functional work, expansion of the targeted resequencing discovery cohort as a prelude to a larger case-control comparison, and incorporation of ENCODE data into analysis of non-coding SNPs may provide critical insights into neuroblastoma pathogenesis.

Citation Format: Andrew C. Wood, Trevor J. Pugh, Olena Morozova, Jan Koster, Jan J. Molenaar, Vanessa Pineros, Kristopher R. Bosse, Juan C. Perin, Sharon Diskin, Maura A. Diamond, Marco Marra, Matthew Meyerson, Rogier Versteeg, John M. Maris. Rare DNA variants are enriched at the BARD1 locus and likely influence neuroblastoma susceptibility. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3804. doi:10.1158/1538-7445.AM2013-3804

A cancer stem cell model for studying brain metastases from primary lung cancer

BACKGROUND

Brain metastases are most common in adults with lung cancer, predicting uniformly poor patient outcome, with a median survival of only months. Despite their frequency and severity, very little is known about tumorigenesis in brain metastases.

METHODS

We applied previously developed primary solid tumor-initiating cell models to the study of brain metastases from the lung to evaluate the presence of a cancer stem cell population. Patient-derived brain metastases (n = 20) and the NCI-H1915 cell line were cultured as stem-enriching tumorspheres. We used in vitro limiting-dilution and sphere-forming assays, as well as intracranial human-mouse xenograft models. To determine genes overexpressed in brain metastasis tumorspheres, we performed comparative transcriptome analysis. All statistical analyses were two-sided.

RESULTS

Patient-derived brain metastasis tumorspheres had a mean sphere-forming capacity of 33 spheres/2000 cells (SD = 33.40) and median stem-cell frequency of 1/60 (range = 0-1/141), comparable to that of primary brain tumorspheres (P = .53 and P = .20, respectively). Brain metastases also expressed CD15 and CD133, markers suggestive of a stemlike population. Through intracranial xenotransplantation, brain metastasis tumorspheres were found to recapitulate the original patient tumor heterogeneity. We also identified several genes overexpressed in brain metastasis tumorspheres as statistically significant predictors of poor survival in primary lung cancer.

CONCLUSIONS

For the first time, we demonstrate the presence of a stemlike population in brain metastases from the lung. We also show that NCI-H1915 tumorspheres could be useful in studying self-renewal and tumor initiation in brain metastases. Our candidate genes may be essential to metastatic stem cell populations, where pathway interference may be able to transform a uniformly fatal disease into a more localized and treatable one.

The genetic landscape of high-risk neuroblastoma

Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%¹. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers.

Cell culture and Drosophila model systems define three classes of anaplastic lymphoma kinase mutations in neuroblastoma

Neuroblastoma is a childhood extracranial solid tumour that is associated with a number of genetic changes. Included in these genetic alterations are mutations in the kinase domain of the anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (RTK), which have been found in both somatic and familial neuroblastoma. In order to treat patients accordingly requires characterisation of these mutations in terms of their response to ALK tyrosine kinase inhibitors (TKIs). Here, we report the identification and characterisation of two novel neuroblastoma ALK mutations (A1099T and R1464STOP), which we have investigated together with several previously reported but uncharacterised ALK mutations (T1087I, D1091N, T1151M, M1166R, F1174I and A1234T). In order to understand the potential role of these ALK mutations in neuroblastoma progression, we have employed cell culture-based systems together with the model organism Drosophila as a readout for ligand-independent activity. Mutation of ALK at position 1174 (F1174I) generates a gain-of-function receptor capable of activating intracellular targets such as ERK (extracellular signal regulated kinase) and STAT3 (signal transducer and activator of transcription 3) in a ligand-independent manner. Analysis of these previously uncharacterised ALK mutants and comparison with ALK^F1174 mutants suggests that ALK mutations observed in neuroblastoma fall into three classes. These classes are: (i) gain-of-function ligand-independent mutations such as ALK^F1174l, (ii) kinase-dead ALK mutants, e.g. ALK^I1250T (Schönherr et al., 2011a) and (iii) ALK mutations that are ligand-dependent in nature. Irrespective of the nature of the observed ALK mutants, in every case the activity of the mutant ALK receptors could be abrogated by the ALK inhibitor crizotinib (Xalkori/PF-02341066), albeit with differing levels of sensitivity.

DNA hypermethylation and 1p Loss silence NHE-1 in oligodendroglioma

Oligodendroglioma is characterized by mutations of IDH and CIC, 1p/19q loss, and slow growth. We found that NHE-1 on 1p is silenced in oligodendrogliomas secondary to IDH-associated hypermethylation and 1p allelic loss. Silencing lowers intracellular pH and attenuates acid load recovery in oligodendroglioma cells. Others have shown that rapid tumor growth cannot occur without NHE-1-mediated neutralization of the acidosis generated by the Warburg glycolytic shift. Our findings show for the first time that the pH regulator NHE-1 can be silenced in a human cancer and also suggest that pH deregulation may contribute to the distinctive biology of human oligodendroglioma.

Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression

Biallelic mutations of the DNA annealing helicase SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1) cause Schimke immuno-osseous dysplasia (SIOD, MIM 242900), an incompletely penetrant autosomal recessive disorder. Using human, Drosophila and mouse models, we show that the proteins encoded by SMARCAL1 orthologs localize to transcriptionally active chromatin and modulate gene expression. We also show that, as found in SIOD patients, deficiency of the SMARCAL1 orthologs alone is insufficient to cause disease in fruit flies and mice, although such deficiency causes modest diffuse alterations in gene expression. Rather, disease manifests when SMARCAL1 deficiency interacts with genetic and environmental factors that further alter gene expression. We conclude that the SMARCAL1 annealing helicase buffers fluctuations in gene expression and that alterations in gene expression contribute to the penetrance of SIOD.

Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers

Oligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p and 19q are strongly associated with this brain cancer but knowledge of the identity and function of the genes affected by these alterations is limited. We performed exome sequencing on a discovery set of 16 oligodendrogliomas with 1p/19q co-deletion to identify new molecular features at base-pair resolution. As anticipated, there was a high rate of IDH mutations: all cases had mutations in either IDH1 (14/16) or IDH2 (2/16). In addition, we discovered somatic mutations and insertions/deletions in the CIC gene on chromosome 19q13.2 in 13/16 tumours. These discovery set mutations were validated by deep sequencing of 13 additional tumours, which revealed seven others with CIC mutations, thus bringing the overall mutation rate in oligodendrogliomas in this study to 20/29 (69%). In contrast, deep sequencing of astrocytomas and oligoastrocytomas without 1p/19q loss revealed that CIC alterations were otherwise rare (1/60; 2%). Of the 21 non-synonymous somatic mutations in 20 CIC-mutant oligodendrogliomas, nine were in exon 5 within an annotated DNA-interacting domain and three were in exon 20 within an annotated protein-interacting domain. The remaining nine were found in other exons and frequently included truncations. CIC mutations were highly associated with oligodendroglioma histology, 1p/19q co-deletion, and IDH1/2 mutation (p < 0.001). Although we observed no differences in the clinical outcomes of CIC mutant versus wild-type tumours, in a background of 1p/19q co-deletion, hemizygous CIC mutations are likely important. We hypothesize that the mutant CIC on the single retained 19q allele is linked to the pathogenesis of oligodendrogliomas with IDH mutation. Our detailed study of genetic aberrations in oligodendroglioma suggests a functional interaction between CIC mutation, IDH1/2 mutation, and 1p/19q co-deletion.

Abstract 926: Whole genome and transcriptome sequencing defines the spectrum of somatic changes in high-risk neuroblastoma

The NCI's Therapeutically Applicable Research to Generate Effective Targets (TARGET) initiative uses state-of-the-art genome-wide approaches to identify therapeutic targets for pediatric cancers. Applications of 2nd-generation sequencing technologies to the analysis of adult solid tumors and hematopoietic malignancies have led to novel, often clinically relevant insights into these diseases. The objective of this study is to utilize 2nd-generation sequencing approaches on a highly annotated set of ten high-risk neuroblastomas (NBLs). We performed whole genome shotgun sequencing of six stage 4 MYCN-non-amplified and four stage 4 MYCN-amplified NBL TARGET cases and matched peripheral blood, as well as whole transcriptome sequencing (RNA-Seq) of the corresponding tumor RNA. The tumor and normal genomes were sequenced to 30X haploid coverage, and an average 10.3 Gb of aligned sequence was generated for each tumor transcriptome. The level of sequencing redundancy allowed us to achieve at least 10X coverage across 90% of the genome enabling genome-wide detection of sequence and copy number changes in the tumor DNA. We used alignment and de novo assembly approaches to identify somatic and germline SNVs, indels, structural variants, regions of copy number gains and losses, and genome rearrangements. We used RNA-Seq data to determine whether the detected sequence changes were expressed, and to identify transcripts differentially or alternatively expressed between MYCN-amplified and non-amplified cases. Our analysis of tumor and normal genomes identified an average of 1664 candidate somatic mutations per case, the majority of which were SNVs and small indels falling within introns or intergenic sequence. We also detected two candidate germline mutations in the ALK oncogene, one of which was previously characterized in NBL. An average of 10% of candidate somatic mutations in coding sequence was expressed in the transcriptome representing candidate oncogenic events. In addition, we detected and validated using PCR 9 novel genomic rearrangements resulting in expressed products, 5 of which were somatic and 4 of which were germline. We report on two novel somatic gene fusions, between TRIM37 on chromosome 17 and RNF121 on chromosome 11, and between LSAMP and STAG1 on chromosome 3, previously uncharacterized in NBL. The fusions did not recur in our sample set. This work provides an initial genome-wide view of the landscape of somatic changes that occur in high-risk neuroblastoma and highlights novel candidate oncogenic events that may drive the malignancy. Ongoing efforts will catalogue discovered somatic mutation frequencies in a large set of cases and explore the role of germline DNA variations in NBL tumorigenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 926. doi:10.1158/1538-7445.AM2011-926

Convergent genesis of an adult neural crest-like dermal stem cell from distinct developmental origins

Skin-derived precursors (SKPs) are multipotent dermal stem cells that reside within a hair follicle niche and that share properties with embryonic neural crest precursors. Here, we have asked whether SKPs and their endogenous dermal precursors originate from the neural crest or whether, like the dermis itself, they originate from multiple developmental origins. To do this, we used two different mouse Cre lines that allow us to perform lineage tracing: Wnt1-cre, which targets cells deriving from the neural crest, and Myf5-cre, which targets cells of a somite origin. By crossing these Cre lines to reporter mice, we show that the endogenous follicle-associated dermal precursors in the face derive from the neural crest, and those in the dorsal trunk derive from the somites, as do the SKPs they generate. Despite these different developmental origins, SKPs from these two locations are functionally similar, even with regard to their ability to differentiate into Schwann cells, a cell type only thought to be generated from the neural crest. Analysis of global gene expression using microarrays confirmed that facial and dorsal SKPs exhibit a very high degree of similarity, and that they are also very similar to SKPs derived from ventral dermis, which has a lateral plate origin. However, these developmentally distinct SKPs also retain differential expression of a small number of genes that reflect their developmental origins. Thus, an adult neural crest-like dermal precursor can be generated from a non-neural crest origin, a finding with broad implications for the many neuroendocrine cells in the body.

Selective targeting of neuroblastoma tumour-initiating cells by compounds identified in stem cell-based small molecule screens

Neuroblastoma (NB) is the most deadly extra-cranial solid tumour in children necessitating an urgent need for effective and less toxic treatments. One reason for the lack of efficacious treatments may be the inability of existing drugs to target the tumour-initiating or cancer stem cell population responsible for sustaining tumour growth, metastases and relapse. Here, we describe a strategy to identify compounds that selectively target patient-derived cancer stem cell-like tumour-initiating cells (TICs) while sparing normal paediatric stem cells (skin-derived precursors, SKPs) and characterize two therapeutic candidates. DECA-14 and rapamycin were identified as NB TIC-selective agents. Both compounds induced TIC death at nanomolar concentrations in vitro, significantly reduced NB xenograft tumour weight in vivo, and dramatically decreased self-renewal or tumour-initiation capacity in treated tumours. These results demonstrate that differential drug sensitivities between TICs and normal paediatric stem cells can be exploited to identify novel, patient-specific and potentially less toxic therapies.

LNCaP Atlas: gene expression associated with in vivo progression to castration-recurrent prostate cancer

Background

There is no cure for castration-recurrent prostate cancer (CRPC) and the mechanisms underlying this stage of the disease are unknown.

Methods

We analyzed the transcriptome of human LNCaP prostate cancer cells as they progress to CRPC in vivo using replicate LongSAGE libraries. We refer to these libraries as the LNCaP atlas and compared these gene expression profiles with current suggested models of CRPC.

Results

Three million tags were sequenced using in vivo samples at various stages of hormonal progression to reveal 96 novel genes differentially expressed in CRPC. Thirty-one genes encode proteins that are either secreted or are located at the plasma membrane, 21 genes changed levels of expression in response to androgen, and 8 genes have enriched expression in the prostate. Expression of 26, 6, 12, and 15 genes have previously been linked to prostate cancer, Gleason grade, progression, and metastasis, respectively. Expression profiles of genes in CRPC support a role for the transcriptional activity of the androgen receptor (CCNH, CUEDC2, FLNA, PSMA7), steroid synthesis and metabolism (DHCR24, DHRS7, ELOVL5, HSD17B4, OPRK1), neuroendocrine (ENO2, MAOA, OPRK1, S100A10, TRPM8), and proliferation (GAS5, GNB2L1, MT-ND3, NKX3-1, PCGEM1, PTGFR, STEAP1, TMEM30A), but neither supported nor discounted a role for cell survival genes.

Conclusions

The in vivo gene expression atlas for LNCaP was sequenced and support a role for the androgen receptor in CRPC.

System-level analysis of neuroblastoma tumor-initiating cells implicates AURKB as a novel drug target for neuroblastoma

PURPOSE

Neuroblastoma (NB) is an aggressive tumor of the developing peripheral nervous system that remains difficult to cure in the advanced stages. The poor prognosis for high-risk NB patients is associated with common disease recurrences that fail to respond to available therapies. NB tumor-initiating cells (TICs), isolated from metastases and primary tumors, may escape treatment and contribute to tumor relapse. New therapies that target the TICs may therefore prevent or treat tumor recurrences.

EXPERIMENTAL DESIGN

We undertook a system-level characterization of NB TICs to identify potential drug targets against recurrent NB. We used next-generation RNA sequencing and/or human exon arrays to profile the transcriptomes of 11 NB TIC lines from six NB patients, revealing genes that are highly expressed in the TICs compared with normal neural crest-like cells and unrelated cancer tissues. We used gel-free two-dimensional liquid chromatography coupled to shotgun tandem mass spectrometry to confirm the presence of proteins corresponding to the most abundant TIC-enriched transcripts, thereby providing validation to the gene expression result.

RESULTS

Our study revealed that genes in the BRCA1 signaling pathway are frequently misexpressed in NB TICs and implicated Aurora B kinase as a potential drug target for NB therapy. Treatment with a selective AURKB inhibitor was cytotoxic to NB TICs but not to the normal neural crest-like cells.

CONCLUSION

This work provides the first high-resolution system-level analysis of the transcriptomes of 11 primary human NB TICs and identifies a set of candidate NB TIC-enriched transcripts for further development as therapeutic targets.

SKPs derive from hair follicle precursors and exhibit properties of adult dermal stem cells

Despite the remarkable regenerative capacity of mammalian skin, an adult dermal stem cell has not yet been identified. Here, we investigated whether skin-derived precursors (SKPs) might fulfill such a role. We show that SKPs derive from Sox2(+) hair follicle dermal cells and that these two cell populations are similar with regard to their transcriptome and functional properties. Both clonal SKPs and endogenous Sox2(+) cells induce hair morphogenesis, differentiate into dermal cell types, and home to a hair follicle niche upon transplantation. Moreover, hair follicle-derived SKPs self-renew, maintain their multipotency, and serially reconstitute hair follicles. Finally, grafting experiments show that follicle-associated dermal cells move out of their niche to contribute cells for dermal maintenance and wound-healing. Thus, SKPs derive from Sox2(+) follicle-associated dermal precursors and display functional properties predicted of a dermal stem cell, contributing to dermal maintenance, wound-healing, and hair follicle morphogenesis.

Abstract 12: Metastatic neuroblastoma cancer stem cells display a mixed phenotype of tumor and niche origin required for survival

Neuroblastoma (NB) is a pediatric tumor of neural crest origin, and is the most common cancer of infancy. 50% of patients have metastases at diagnosis, of which 85% will die after multiple relapses from metastatic disease. We identified tumor-initiating cells (TICs) from bone marrow (BM) metastases of high-risk patients that are propagated as spheres and that have many properties of cancer stem cells, and form NB in mice with as few as 1 cell. To understand patient relapse and disease progression, we compared NB-TICs from BM with those from tumor and brain metastases and SKPs, a normal pediatric stem cell counterpart, by cDNA microarray, flow cytometry, and whole genome shotgun sequencing transcriptome analysis. BM-derived NB-TICs expressed primitive neural crest and neuronal markers as well as hematopoietic markers from primitive, myeloid, and B-cell lineages and contained VDJ gene rearrangements, which are normally associated with B-cell leukemias. Hematopoietic genes were not expressed or expressed at very low levels in tumor-derived sphere lines and a line from an NB brain metastasis, however brain metastasis-derived TICs expressed CD133, while BM-derived NB-TICs did not. Furthermore, we found that shRNA to CD74, which is upregulated in B-cell lymphoma and multiple myeloma and is a therapeutic target for those cancers, induced the rapid death of NB-TICs but not normal SKPs. Interestingly cells co-staining for the hematopoietic markers CD45 or CD74 and the neural neural progenitor marker nestin were found in BM smears of patients with relapsed NB in the bone marrow.

We suggest that metastatic TICs from some tumors adopt resident niche-specific gene expression signatures, which may aid diagnosis and the development of novel treatments. We hypothesize that drugs used for leukemia may be efficacious therapeutics for metastatic NB, and are currently testing this hypothesis in mouse models.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 12.

From gastroprotective to proulcerogenic action of glucocorticoids on the gastric mucosa

Glucocorticoids may have dual action on the gastric mucosa: physiological gastroprotective and pathological proulcerogenic one. In the present study we investigated how gastroprotective action of glucocorticoids can be transformed to proulcerogenic effect. Dose- and time-dependent effects of single injection of dexamethasone on cold-restraint-induced gastric erosions, corticosterone and blood glucose levels, somatic parameters were investigated in fasted rats. Dexamethasone at a dose of 1 mg/kg decreased the gastric erosion area and maintained blood glucose level in fasted rats in the case of its injection 1 h before the stress. A dose of 1 mg/kg has been selected for the time-dependent study. The results demonstrate that single injection of dexamethasone at a dose of 1 mg/kg may attenuate or aggravate cold-restraint-induced gastric erosions depending on the time of the injection before the stress. Gastroprotective action of dexamethasone was observed in the case of its injection 1 and 12 h before cold-restraint. The further increase in the time interval caused transformation of gastroprotective action of dexamethasone to proulcerogenic effect. Both short-term and long-term dexamethasone action resulted in maintenance of blood glucose level in fasted rats. The results suggest that glucocorticoid-induced long-lasting maintenance of blood glucose levels accompanied with the signs of their catabolic effect and dexamethasone-induced corticosterone deficiency may be responsible, at least partly, for the transformation of gastroprotective action of glucocorticoids to their proulcerogenic effect.

Genomic analysis distinguishes phases of early development of the mouse atrio-ventricular canal

Valve formation during embryonic heart development involves a complex interplay of regional specification, cell transformations, and remodeling events. While many studies have addressed the role of specific genes during this process, a global understanding of the genetic basis for the regional specification and development of the heart valves is incomplete. We have undertaken genome-wide transcriptional profiling of the developing heart valves in the mouse. Four Serial Analysis of Gene Expression libraries were generated and analyzed from the mouse atrio-ventricular canal (AVC) at embryonic days 9.5-12.5, covering the stages from initiation of endothelial to mesenchymal transition (EMT) through to the beginning of endocardial cushion remodeling. We identified 14 distinct temporal patterns of gene expression during AVC development. These were associated with specific functions and signaling pathway members. We defined the temporal distribution of mesenchyme genes during the EMT process and of specific Notch and transforming growth factor-beta targets. This work provides the first comprehensive temporal dataset during the formation of heart valves. These results identify molecular signatures that distinguish different phases of early heart valve formation allowing gene expression and function to be further investigated.